49ers quarterback Colin Kaepernick (7) runs for a touchdown against the New Orleans Saints during the first quarter on Sunday. / Derick E. Hingle, US Presswire

by Robert Klemko, USA TODAY Sports

by Robert Klemko, USA TODAY Sports

NEW ORLEANS â?? Colin Kaepernick dressed slowly, pulling a deep red dress shirt over his tattooed torso as teammates streamed by, congratulating him on his second win as an NFL starter.

To Kaepernick's right sat his reluctant counterpart in the league's biggest quarterback controversy, former starter Alex Smith. And after Kaepernick's performance led the San Francisco 49ers to a 31-21 win over the New Orleans Saints, the former backup doesn't figure to give Smith his job back anytime soon.

Smith, drafted No. 1 overall by the team in 2005, palmed a football on the sidelines and watched without a smile as a 25-year-old, second-round draft pick out of Nevada took his place under center, extending passing plays with his feet and tossing darts with his right arm.

Riding a dominant defensive performance, Kaepernick earned win No. 2 as a starter. Coach Jim Harbaugh's decision to replace Smith with Kaepernick came two weeks after Smith went down with a concussion (Smith was cleared to play Sunday). Kaepernick has since passed for 474 yards, three touchdowns and one interception in victories vs. the Chicago Bears and the Saints, which puts the 49ers at 8-2-1 with five games to play.

The soft-spoken Kaepernick said the victories over two playoff contending teams have boosted his confidence to a new place.

"Moving forward I'll have great confidence no matter what happens," Kaepernick said. "I'm just going to keep my head down and keep working and see where it takes me."

Saints interim coach Joe Vitt had kind words for the quarterback following a 231-yard, two-touchdown performance.

"He does a good job," Vitt said. "He makes plays on his feet. He extends the down. He's got a pretty good knowledge of the offense. He's got a good tempo. He did a good job. Give him credit."

Harbaugh's offense with Kaepernick employed some of the same principles of the Washington Redskins' zone-read scheme with rookie Robert Griffin III. Kaepernick sprinted into the end zone for a 7-yard touchdown on the game's second drive, faking a handoff and weaving his way across the left side of the field.

"He has a real knack for it," Harbaugh said of Kaepernick's option play. "He has a special ability, honed it in college and has taken it to the pro level. He can cover ground real fast, and he has an eye for making the read. He came with that ability. I take no credit for that one."

It was a far cry from the more conservative attack the 49ers have settled for under Smith, labeled a game manager by most. Smith had been the NFL's quarterback most likely to take a sack or throw away a pass when under pressure in 2012, according to data compiled by profootballfocus.com. He was leading the NFL in completion percentage before getting injured and benched, and was 20-5-1 under Harbaugh, who would not reveal his starter until an hour before game time.

Harbaugh similarly would not say who his starter will be Sunday at St. Louis.

Despite leading San Francisco to the NFC Championship Game last season, and being a couple special teams gaffes away from the Super Bowl, Smith wasn't standing on the firmest ground in San Francisco. The team sought free agent and former Indianapolis Colts quarterback Peyton Manning in March before Manning chose the Denver Broncos.

Kaepernick struggled with communication issues early, as the Superdome crowd turned up the volume on the passer in his second start. The last time Kaepernick started a game indoors, he threw five touchdowns and the Nevada Wolfpack won 63-17 at Idaho's 16,000-seat Kibbie Dome. This wasn't quite as easy.

"It was real loud at times, and we had to work on communicating the plays early on to be effective," Kaepernick said. "I had to audible a lot to communicate to the guys what we were doing. Other than that, the offense played the way it should."

After a low shotgun snap in the second quarter, Kaepernick threw an interception to Patrick Robinson at midfield as the 49ers drove in an attempt to cut down a 14-7 Saints lead. But New Orleans quarterback Drew Brees threw an interception two plays later to Ahmad Brooks that was returned for a touchdown, Brees' first of two pick sixes on the day. Brees also was sacked five times, including 1.5 each for Brooks, Aldon Smith and Justin Smith.

Kaepernick otherwise found success against a pass defense ranked second worst in the NFL heading into Week 12. He threw a third-quarter touchdown pass to Frank Gore to a cap a six-play, 80-yard scoring drive.

The resurgent Saints were riding a three-game winning streak and could've been in line for the No. 6 seed in the NFC after losses by the Buccaneers, Seahawks and Vikings. Now 5-6, New Orleans heads to Atlanta on Thursday for a game critical to the Saints' playoff aspirations.